README for MCPrimers.pm V 1.03 and mcprimers

1. Authorship and copyright

Author:    Stephen G. Lenk, November 2005
Copyright: Stephen G. Lenk (C) 2005. All rights reserved. 

This program is free software; you can redistribute it and/or  
modify it under the same terms as Perl itself.
Licenced under the Perl Artistic Licence.

############################################################################
# This software comes with no guarantee of usefulness.
# Use at your own risk.
# There is no guarantee this code will find the best solution, or even any 
# solution, or that the solutions it finds will be correct or useful to you.
#
# Use at your risk. Check any solutions you obtain.
#
# Stephen G. Lenk assumes no responsibility for the use of this software.
############################################################################

Primer3 is called by this code to verify that the PCR primers are OK.
Primer3 is Copyright (c) 1996,1997,1998,1999,2000,2001,2004
Whitehead Institute for Biomedical Research. All rights reserved.

2. Installation

MCPrimers.pm  - Place into Perl Bio/MCPrimers.pm.
mcprimers.bat - Front end script for MSWindows 
mcprimers     - Rename as mcprimers for other OS (OSX, etc)

PRIMER3DIR -   set this environment variable to point to Primer3 executable.
If PRIMER3DIR is not set, MCPrimers will set it to '.' by default.

MSWindows -    use primer3.exe
Other OS  -    use primer3_core, have IPC::Open3 in search path

3. Purpose

Creates molecular cloning PCR primer pairs for a given gene so that the
gene can be directionally inserted into a vector. pET-32a is the only
vector currently supported. Solver is generic, restriction enzymes and 
their order in the vector are specified in the caller.

4. Use

Use:     mcprimers [options] dna.fasta > result.pr3
Options: [-h] [-s search_shift] [-all] [-clamp (both | 3prime)]

-h        help
-s        integer value to shift search of left RE match into gene
          use -s 24 (or other value) if initial search fails
-all      generate all solutions the MCPrimer heuristic will generate
-clamp    GC clamp
          'both' will clamp last NT at both ends to G or C (default)
          '3prime' will clamp last NT on 3' ends to G or C
          
Example:  mcprimers -s 12 -clamp 3prime -all ppib.fa > ppib_all.pr3

---------------

Enjoy,

Steve Lenk
slenk@emich.edu